3KCG

Crystal structure of the antithrombin-factor IXa-pentasaccharide complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth H]	d3kcgh_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Coagulation factor IXa, protease domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth I]	d3kcgi_	Multi-domain proteins (alpha and beta)	Serpins	Serpins	Serpins	Antithrombin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth L]	d3kcgl_	Small proteins	Knottins (small inhibitors, toxins, lectins)	EGF/Laminin	EGF-type module	Factor IX (IXa)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth H]	SCOP2B Superfamily	Trypsin-like serine proteases	8042263	3000114	SCOP2B (2022-06-29)
C [auth I]	SCOP2B Superfamily	Serpins	8037674	3001563	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth H]	Trypsin_1	e3kcgH1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin_1	ECOD (1.6)
C [auth I]	Serpin	e3kcgI1	A: a+b complex topology	X: Serpins (From Topology)	H: Serpins (From Topology)	T: Serpins	F: Serpin	ECOD (1.6)
A [auth L]	FXa_inhibition	e3kcgL1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: FXa_inhibition	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth H]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
C [auth I]	3.30.497.10	Alpha Beta	2-Layer Sandwich	Antithrombin	Chain I, domain 2	CATH (4.3.0)
C [auth I]	2.30.39.10	Mainly Beta	Roll	Alpha-1-antitrypsin	domain 1	CATH (4.3.0)
A [auth L]	2.10.25.10	Mainly Beta	Ribbon	Laminin	Laminin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth H]	PF00089	Trypsin (Trypsin)	Trypsin	-	Domain
C [auth I]	PF00079	Serpin (serine protease inhibitor) (Serpin)	Serpin (serine protease inhibitor)	Structure is a multi-domain fold containing a bundle of helices and a beta sandwich.	Domain
A [auth L]	PF14670	Coagulation Factor Xa inhibitory site (FXa_inhibition)	Coagulation Factor Xa inhibitory site	This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth H]	Coagulation factor IXa heavy chain	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding proteolysis metabolic process cellular process multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process zymogen activation gene expression macromolecule biosynthetic process protein maturation biosynthetic process protein processing	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix plasma membrane membrane intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen cytoplasm endoplasmic reticulum lumen endoplasmic reticulum
C [auth I]	Antithrombin-III	enzyme regulator activity molecular function inhibitor activity peptidase regulator activity serine-type endopeptidase inhibitor activity molecular function regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity protein binding binding enzyme binding protease binding heparin binding enzyme regulator activity molecular function inhibitor activity peptidase regulator activity serine-type endopeptidase inhibitor activity molecular function regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity protein binding binding enzyme binding protease binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding identical protein binding	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding regulation of biological process regulation of response to external stimulus regulation of blood coagulation multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding regulation of biological process regulation of response to external stimulus regulation of blood coagulation response to external stimulus regulation of coagulation regulation of response to wounding regulation of response to stimulus regulation of response to stress regulation of wound healing regulation of multicellular organismal process regulation of hemostasis	cellular anatomical structure extracellular region extracellular space blood microparticle membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle cellular anatomical structure extracellular region extracellular space blood microparticle membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm extracellular exosome extracellular vesicle extracellular organelle vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix plasma membrane membrane
A [auth L]	Coagulation factor IXa light chain	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding proteolysis metabolic process cellular process multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process zymogen activation gene expression macromolecule biosynthetic process protein maturation biosynthetic process protein processing	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix plasma membrane membrane intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen cytoplasm endoplasmic reticulum lumen endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth H]	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
B [auth H]	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
B [auth H]	IPR000742	EGF-like domain	Domain
B [auth H]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
B [auth H]	IPR050442	Peptidase S1 family, coagulation factors	Family
B [auth H]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B [auth H]	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
B [auth H]	IPR001314	Peptidase S1A, chymotrypsin family	Family
B [auth H]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
B [auth H]	IPR001254	Serine proteases, trypsin domain	Domain
B [auth H]	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
B [auth H]	IPR001881	EGF-like calcium-binding domain	Domain
B [auth H]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
B [auth H]	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
B [auth H]	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family
C [auth I]	IPR023795	Serpin, conserved site	Conserved Site
C [auth I]	IPR000215	Serpin family	Family
C [auth I]	IPR033829	Antithrombin-III, serpin domain	Domain
C [auth I]	IPR023796	Serpin domain	Domain
C [auth I]	IPR042178	Serpin superfamily, domain 1	Homologous Superfamily
C [auth I]	IPR042185	Serpin superfamily, domain 2	Homologous Superfamily
C [auth I]	IPR036186	Serpin superfamily	Homologous Superfamily
A [auth L]	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
A [auth L]	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
A [auth L]	IPR000742	EGF-like domain	Domain
A [auth L]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
A [auth L]	IPR050442	Peptidase S1 family, coagulation factors	Family
A [auth L]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth L]	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
A [auth L]	IPR001314	Peptidase S1A, chymotrypsin family	Family
A [auth L]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A [auth L]	IPR001254	Serine proteases, trypsin domain	Domain
A [auth L]	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
A [auth L]	IPR001881	EGF-like calcium-binding domain	Domain
A [auth L]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A [auth L]	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
A [auth L]	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth H]	Pharos: P00740	hemophilia B hemophilia A thrombophilia, X-linked, due to factor 9 defect coumarin resistance malignant mesothelioma thrombophilia thrombotic disease Autosomal Hemophilia A hemophilia bipolar disorder psoriasis vascular disease congenital factor XI deficiency
C [auth I]	Pharos: P01008	antithrombin III deficiency nephrotic syndrome Venous Thrombosis intracranial thrombosis disseminated intravascular coagulation adult acute respiratory distress syndrome venous thromboembolism acute coronary syndrome intracerebral hemorrhage thrombotic disease acute liver failure malignant glioma cerebrovascular disorder thrombocytopenia hypertensive disorder antithrombin III deficiency nephrotic syndrome Venous Thrombosis intracranial thrombosis disseminated intravascular coagulation adult acute respiratory distress syndrome venous thromboembolism acute coronary syndrome intracerebral hemorrhage thrombotic disease acute liver failure malignant glioma cerebrovascular disorder thrombocytopenia hypertensive disorder blood coagulation disease coronary artery disease thrombophilia heart disease brain injury pulmonary embolism
A [auth L]	Pharos: P00740	hemophilia B hemophilia A thrombophilia, X-linked, due to factor 9 defect coumarin resistance malignant mesothelioma thrombophilia thrombotic disease Autosomal Hemophilia A hemophilia bipolar disorder psoriasis vascular disease congenital factor XI deficiency